Once Upon a Time Machine 3-1: Witches and Warriors
by Doctor's Torchwood
Summary: The Doctor and his new magical companion visit Storybrooke and discover a plot by the Sontarans to assassinate the new Dark Ones. They try to stop these aliens while also keeping the Master away from the Wicked Witch and her new baby. The danger is real. Can the heroes stop the Sontarans and unravel Missy's devious plans?
1. Witches

_I do not own Doctor Who or Once Upon a Time. Only this story. Enjoy!_

* * *

Chapter 1: Witches

(*FLASHBACK*)

* * *

Enchanted Forest

The Wicked Witch strolled through the halls of the Evil Queen's empty castle once again. Zelena moved into the castle after Regina's curse brought everyone to a land without magic. She decided to make the castle her new home and wait for her sister's inevitable return. She initially wanted to bring a whole army of flying monkeys with her, but she ran into some trouble with the Doctor and Martha Jones back in Oz and was only able to take a few monkeys. The witch walked into Regina's bedroom and looked at the empty kingdom. Her green skin stood out as she wore another one of Regina's dresses. Suddenly, she heard a voice calling from behind her.

"I hate her too." A female voice said.

Zelena turned around and saw a tall woman with brown hair and a long purple coat.

"Who are you?" Zelena asked.

"Missy." She replied. "I hate your sister too."

"How do you know Regina?" Zelena asked. "How do you know she's my sister?"

"I was friends with your mother." Missy said. "Cora told me all about both of you."

"So what are you then?" Zelena asked. "Some kind of witch?"

"Something like that." Missy said.

"Why do you hate Regina?" Zelena asked.

"She's been a constant disruption in my plans." Missy said. "She and the Doctor."

"You know the Doctor?" Zelena said.

"More than you know." Missy said. "I came here because I need your help to destroy the Evil Queen. Your mother was fun, evil, and powerful. Seeing as she's now dead, you're not a bad second choice. Plus you have a bloodlust for revenge against her."

"What do you need my help with?" Zelena asked.

"I need your help procuring a weapon from a far away land." Missy said.

"What will this weapon do?" Zelena asked.

"Destroy your sister." Missy said. "Do we have a deal?"

"We certainly do." Zelena said with a villainous smirk.

* * *

(*PRESENT DAY*)

* * *

Storybrooke

Missy stood at the town line. It was night in Storybrooke. The area around the tine line was deserted, as it normally was. Missy kept checking her watch. She was waiting for her accomplices to arrive. She hoped they wouldn't be too much longer. She really wanted to get started. Suddenly, there were two flashes of light in front of her that teleported two Sontaran soldiers with laser guns.

"Well it's about time you two got here." Missy said. "I paid a handsome bargain to acquire your services. I assumed you'd be on time."

"You have selected our services to assassinate someone." The first Sontaran said.

"I picked the best warriors in the galaxy." Missy said. "And I don't want you to kill one person. I want you to kill two people."

"Who?" The second Sontaran asked.

"The Dark Ones." Missy said. "Emma Swan and Killian Jones."

Missy then handed them two small devices that looked like iPhones.

"What are these?" The first Sontaran asked.

"These are special trackers." Missy said. "They will allow you to locate centers of extreme dark magic. They will lead you to the Dark Ones."

"What will you do?" The second Sontaran asked.

"I need to find my old friend Zelena." Missy said. "We have a lot to catch up on. Now run along and kill the Dark Ones before the Doctor gets here with whatever chippy girl he's with nowadays."


	2. A New Companion

Chapter 2: A New Companion

(*FLASHBACK*)

* * *

Arendelle

Missy and Zelena appeared in a cloud of magic smoke in downtown Arendelle. The people around them gave them strange looks as they walked by. There was a slight chill in the air and a little snow was falling.

"Where are we?" Zelena asked.

"Arendelle." Missy said. "Just across the sea from the Enchanted Forest."

"What weapon are we looking for that will destroy my sister?" Zelena asked.

"Look around." Missy said.

"It's snowing." Zelena said. "Why is it snowing? It's the middle of summer."

"There's a woman here with the power to change the weather." Missy said. "Her name is Elsa. The Evil Queen will stand no chance against her ice magic."

"Where is she?" Zelena asked.

"The Royal Castle." Missy said. "She's the Queen of Arendelle. Let's pay her a visit."

* * *

(*PRESENT DAY*)

* * *

The Doctor strutted around the TARDIS as his newest companion watched. After Clara left and the Doctor lost much of his memories about her, the old Time Lord stumbled on a new companion in a magical kingdom he had visited before. She watched in amazement as the Doctor maneuvered around the TARDIS console. She herself was also a sight to behold. Her blonde hair glowed and her bright blue dress was elegant. Not to mention her special magic powers. The Doctor was now traveling through time and space with Queen Elsa of Arendelle.

"So where are we going?" Elsa asked.

"A town called Storybrooke." The Doctor said.

"Storybrooke?" Elsa asked. "Why there?"

"You've heard of it?" The Doctor asked.

"Yes." Elsa said. "I was there last year. It's a long story. So why are we going there."

"According to the TARDIS, there's some kind of alien presence there. Aliens and magic never mix well." The Doctor said.

"What kind of alien?" Elsa asked.

"They're called Sontarans." The Doctor said. "They're a deadly, warlike race. Are you up for this?"

"Of course I am." Elsa said.

* * *

Storybrooke

Things were especially stressful in the Storybrooke Hospital tonight. Zelena was only two months pregnant when she magically went into labor. She gave birth to her daughter while in intense pain. No one knew what caused this. Dr. Whale was cleaning the baby in the room. Robin Hood and Regina stood over Zelena as she laid in her hospital bed, recovering from the trauma of birth.

"I want to hold her." Zelena said. "I want to hold my baby."

"You're never going anywhere near her." Robin Hood said.

"How did this happen?" Regina asked.

"Dark magic." Zelena said.

"But you said you didn't do anything." Robin said.

"I didn't." Zelena said. "Take a wild guess who did."

"The Dark One." Robin said.

"Emma?" Regina asked. "Why would she speed up your pregnancy?"

"Excellent question." Emma Swan said as she appeared in the doorway. This evil Emma wore all black clothes and wore her hair in a tight bun.

"Why did you do this?" Regina asked. "Why do this to a baby?"

"The opposite is true." Emma said. "I saved the baby. She is innocent in all this. Now that she has been born, her mother can be used for the greater good."

"Not my style." Zelena said from the bed.

"The only way to get the darkness out of me is to use Excalibur and put it into someone else." Emma said.

"And you think that person should be Zelena?" Robin asked. "You want the next dark one to be the Wicked Witch?"

"Once the darkness is in her, I can kill her with Excalibur and destroy the darkness forever. I live, she dies, and there will never be a dark one ever again. Everybody wins." Emma said.

"No." Regina said. "That's not how we do things."

"Well for once I'm the more powerful one Regina." Emma said. "You can't stop me."

Suddenly, the glass window in the room was shattered by a laser blast. Then, a Sontaran soldier hopped into the window and looked at everyone in the room. Regina was shocked with horror to see a Sontaran again. She had a rather...complicated history with them. After forcing them to be her slaves to hunt Snow White back in the Enchanted Forest, an army of them invaded the forest and tried to kill her. If not for the Doctor and Clara Oswald, they just might have. Now one was here again all these years later.

"What the hell are you doing here?" Regina asked as she conjured a ball of fire.

"Emma Swan." The Sontaran asked. "You are the Dark One. I've been assigned to eliminate you. Prepare to die."

Emma then disappeared in a cloud of magic smoke. Regina then launched her fireball at the Sontaran. The impact of the blast did not kill the Sontaran, but was enough to force him flying out the window. Robin and Regina then rushed to the window to look at the creature outside. However, they saw nothing. It has escaped into the night. Before they could process what just happened, something else strange started to occur. There was a strange wind in the hospital room accompanied by a loud wheezing type sound. Regina, Robin, and Zelena had all heard this sound before. This was the sound of the TARDIS. They all watched as the famous blue box began materializing in the corner of the room by the entrance.


	3. Brawl

Chapter 3: Brawl

(*FLASHBACK*)

* * *

Arendelle

Missy and Zelena walked through the town of Arendelle. They got strange looks from everyone. Missy for her strange clothes and Zelena for her green skin. Zelena was used to dealing with people staring at her, but today she was just too annoyed. She walked over to a man. He was likely a baker since he was standing outside a bakery sweeping the front steps. Zelena did not care for such minor details. She used her magic to lift the man into the air.

"Listen you little man." The Wicked Witch said. "I don't have time for everyone to stare at me like some kind of freak. I came here because I need something and you're going to tell me where it is."

The man couldn't talk. He was paralyzed with fear. He could see the determination in Zelena's eyes. Missy then walked up next to Zelena so she could address the man.

"I'd listen to her if I were you." Missy said. "Where is Queen Elsa?"

"Right here!" Elsa shouted from across the square.

Zelena and Missy turned around and saw Queen Elsa. She looked furious. Standing behind her was her sister Anna and Anna's husband Kristoff. They had all been taking a walk through the city. When Elsa spotted what these foreigners were doing to her citizens, she immediately got involved. Zelena released her hold on the man and he fell to the ground. Then he quickly got up and ran away.

"You must be the famous Queen I've heard so much about." Zelena said.

"And who are you that dares to come to my city and abuse my citizens?" Elsa asked in a commanding voice.

"Call me Missy." The Time Lady said. "This is Zelena. Forgive us. We were just trying to get your attention."

"Well you've got it." Elsa fired back.

"Relax dear." Missy said. "We only want to talk."

"You want to talk?" Elsa asked. "Then why are you attacking my people?"

"It's ok Elsa." Anna said. "They just want to talk."

"Stay out of this." Elsa said.

"Don't talk to her that way." Kristoff said.

"Not now." Elsa said.

"I'd hate to interrupt your family squabble, but we've come a long way." Zelena said.

"Fine." Elsa said. "What do you want?"

"You." Missy said. "We're trying to destroy an enemy of ours and we want your help to do it."

"What enemy?" Elsa asked.

"They call her the Evil Queen." Zelena said. "Surely you'd want to help eliminate someone like that."

"Why should I believe you." Elsa said.

"Elsa." Anna said. "They're asking for your help."

"I don't trust them." Elsa said. "If they were noble then they wouldn't have harmed any of my people."

"Well talking didn't work." Zelena said to Missy. "Time to try it my way."

Zelena then raised her arm high. At the same time, Anna started to levitate in the air.

"You put her down right down!" Elsa shouted.

"No harm will come to her as long as you agree to help us." Zelena warned.

Missy noticed that the clouds started to darken and it began to lightly snow out of nowhere.

"I said put her down now." Elsa repeated.

The wind and the snow suddenly grew more intense, but Zelena would not back down. In a fit of rage, Elsa thrusted her arms forward, unleashing a powerful blast if ice magic. Zelena saw she stood no chance of deflecting such a powerful blast. So, she consumed herself in a magic smoke, along with Missy, and transported them away from Arendelle. Once Zelena and Missy were gone, Anna returned to the ground.

"Are you ok?" Kristoff asked her.

"Yes I'm fine." Anna said.

"I knew we couldn't trust them." Elsa said. "If they're smart, they'll never come back here. I hope I never see those two again."


	4. Tension and Confusion

Chapter 4: Tension and Confusion

(*PRESENT DAY*)

* * *

Storybrooke

Regina, Zelena, Robin Hood, and Dr. Whale watched as the TARDIS materialized by the door of the hospital room. Regina had encountered several versions of the Doctor in her lifetime. She wondered which face this Time Lord would be wearing this time. Zelena encountered the Doctor only once before back in Oz, when he was in his tenth incarnation with Martha Jones. Robin Hood also encountered the Tenth Doctor in the Enchanted Forest when he helped rescue Rose Tyler from Maleficent. Now that he was back, the three of them didn't know what to expect. When the blue box finished forming, an old man stepped out. Regina knew him as the twelfth Doctor. She hadn't seen him since they stopped the Master and her army of Cybermen from destroying Storybrooke. The Doctor was very perplexed by what he saw. He hadn't seen the Wicked Witch in hundreds of years. Now here she was in Storybrooke. Her skin was no longer green and she was wearing a black wrist band that inhibited her magic. Robin and Zelena figured the Doctor must have gotten much older. It only added to the confusion when Queen Elsa walked out of the TARDIS as well. She was happy to see Regina again and shocked to see Zelena laying in the hospital bed. The Doctor was especially curious to see Dr. Whale holding a newborn baby girl.

"Hello Doctor." Regina said. "I'm glad you're here. We were just attacked by a Sontaran."

"Sontarans?" The Doctor questioned. "What could they possibly be doing here?"

"Apparently they're hunting the Dark One." Regina said.

"Where is Rumplestiltskin then?" The Doctor asked.

"Actually Emma Swan is the Dark One now." Regina said.

"What?" Elsa asked. "How can that be possible?"

"It's a long story." Regina said.

"And what is she doing here?" The Doctor asked referring to Zelena.

"That's also a long story." Regina said.

"And is that her baby?" The Doctor asked.

"Don't you dare touch her." Zelena said.

"I see you're still as rude as ever." Elsa said.

"Hush you." Zelena said. "Why are you with him anyway? Whatever happened to dear Martha Jones, Doctor?"

"The Doctor invited me to join him on his adventures." Elsa said.

"Martha left me." The Doctor replied. "Now she's married and happily living her life."

"What about Clara?" Regina asked. "Where is she?"

"We should be looking for Emma." The Doctor said, avoiding the subject of Clara at all costs.

"Clara?" Elsa asked. "Is that the one you told me about?"

"We don't have time to delve into this right now." The Doctor said. "We need to stop the Sontarans."

"But why would the Sontarans want to kill the Dark One?" Regina asked.

"We need to find out." The Doctor said.

"You can use the TARDIS to locate them can't you?" Regina asked.

"Indeed." He replied.

"Right then." Regina said as she turned to Robin. "I'm going with him to go after Emma and the Sontarans."

"Then I'm coming with you." Robin said.

"You can't." Regina said. "Someone has to stay here and guard Zelena and the baby."

"Take this band off me." Zelena said. "Then I can protect my daughter all by myself."

"As if we'd ever let you have your magic again." Robin said.

"Please just stay here." Regina said.

"Fine." Robin said. "Just be careful."

With that, the Doctor, Elsa, and Regina entered the TARDIS. Robin, Zelena, and Dr. Whale watched as the old blue box dematerialized before their eyes. As they stood inside the hospital caring for the newborn child, something was happening outside the hospital. Missy was walking up to the building on this dark night. While the Sontarans were after the Dark One, she was free to find her old partner. The Master walked into the hospital with purpose. She was on a mission to find the Wicked Witch.


	5. The Dark Ones

Chapter 5: The Dark Ones

(*FLASHBACK TO THE ENCHANTED FOREST*)

* * *

Zelena and Missy appeared back in Regina's empty castle in a cloud of magic green smoke. They had just been to Arendelle and attempted to get the help of Queen Elsa in getting revenge on the Evil Queen. Unfortunately, the Ice Queen refused to be a part of their evil plan and fought them off. They were forced to retreat back here.

"Well that was a bust." Zelena said.

"That's ok." Missy said. "We'll figure something else out."

"Actually, there is no 'we' anymore." Zelena said. "That was a complete and utter waste of my time. Regina will be returning to this castle soon. I have my own plan for revenge against her. I don't need you."

"Don't cross me witch." Missy said.

"I don't need you." Zelena said. "I never did. You needed me. If you ever want my help again with something that will actually work, feel free to reach out. Until then, you can leave."

"Fine." Missy said. "I was going to use my vortex manipulator to take you back in time and stop Regina from being born, but since you don't want my help…"

"What?" Zelena said, very curious.

However, Missy pressed a button her wrist and was consumed by a bright blue light. Then, she disappeared. She teleported away, leaving an angry Zelena alone in Regina's castle.

* * *

(*PRESENT DAY IN STORYBROOKE*)

* * *

In the forest surrounding Storybrooke on this dark night, Emma Swan and Killian Jones stood alone. Emma had just told Captain Hook that in order to save his life back in Camelot, she turned him into a Dark One. Now, the both of them had incredible dark power. Killian was taken aback by this information. However, before he really had an opportunity to respond to Emma, they suddenly heard a familiar sound. It was a loud, wheezing type sound. Both of them were surprised to once again hear the sound of the TARDIS racing through the night. The magic blue box appeared a few yards away from them.

"What is the Doctor doing here?" Hook asked.

"As long as he doesn't get in my way I don't care." Emma said.

The box finished forming. Then, the Doctor, Regina, and Elsa walked outside and stood in front of the TARDIS.

"Doctor? Elsa? What are you doing here?" Hook asked.

"There are Sontarans in Storybrooke." The Doctor said.

"I know." Emma said. "Apparently they've come to kill the Dark One."

"I can't believe you're the Dark One now." Elsa said.

"I suppose that means I better watch out too." Hook said.

"What do you mean?" Regina asked.

"I'm also the Dark One now." Hook said.

"What?" Regina said.

"How is that possible?" The Doctor asked. "Two Dark Ones?"

"Where are the Sontarans now?" Emma asked.

"We don't know." Regina said. "They could be anywhere."

Suddenly, two Sontaran soldiers appeared out of nowhere. They were hiding in the trees, waiting to strike.

"Dark Ones!" One of the Sontarans shouted. "Prepare to die."


	6. Battle of the Sontarans

Chapter 6: Battle of the Sontarans

Storybrooke

The Doctor, Elsa, Regina, Emma, and Hook stood in the forest at night next to the TARDIS. Two Sontaran soldiers suddenly appeared and were preparing to attack the Dark Ones.

"What are you two doing here?" The Doctor shouted.

"Our mission is to eliminate the Dark Ones." A Sontaran said.

"What have they done to you?" Regina asked.

"We were assigned to kill the Dark Ones." The other Sontaran said.

"By who?" Emma asked. "Who sent you?"

"Silence!" The Sontaran shouted.

Then, the two Sontarans fired several laser blasts at the Dark Ones. However, as the Dark Ones, Emma and Hook were far more powerful than a couple of laser guns. All Emma did was raise her hand in the air. As they did, the Sontaran laser blasts were blown upwards and over their heads by powerful magic. Hook then conjured a magic ball of glowing purple energy on his hand. He didn't even know he could do that. His instincts as the Dark One were kicking in. Then Hook fired a powerful magic blast of purple magic energy at one of the Sontarans. It hit the alien directly and killed it instantly. Then, he did the same thing to the other Sontaran. The battle was over as quickly as it had begun. The Dark One's triumphed over the Sontarans while barely lifting a finger.

"You didn't have to kill them." Elsa said.

"It was them or us." Emma said. "They made that very clear."

"You defeated them with no effort at all." The Doctor said.

"What did you expect?" Hook said. "We're the Dark Ones."

"Exactly." The Doctor said. "Whoever sent the Sontarans to kill you clearly didn't expect them to win."

"Why send assassins if you know they're going to fail?" Regina asked.

"Because they wanted the Dark Ones distracted." The Doctor said.

"Who would do that?" Elsa said.

"It must be someone in Storybrooke." Regina said. "They want the most powerful people in town distracted while they do something else. We need to get back to the hospital and check on Zelena. I fear this has something to do with her."

"Well then let's go." The Doctor said. "Everyone back in the TARDIS."

"I could use magic to get us there faster." Emma said.

"Just get in the TARDIS." The Doctor said. "Your dark magic has done enough for one night."

The Doctor, Elsa, Regina, Emma, and Hook then piled into the TARDIS. They had to rush to get back to the hospital. They had no idea that Missy was the one behind the Sontaran attack. She needed the Dark Ones distracted so she could have Zelena all to herself. Missy walked through the front doors of the hospital now and was about to see her old friend the Wicked Witch.

* * *

 _To be continued. Missy reunites with Zelena and reveals her evil plan. Can the Doctor and his Storybrooke friends stop them? The last chapters should be up soon. Thanks for reading. I hope you enjoyed. Please review and let me know what you think._


End file.
